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| Status |
Public on Jul 26, 2019 |
| Title |
H3K4me1.d3F.r1 |
| Sample type |
SRA |
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| Source name |
mesendoderm cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: double knock-in (DKI) mouse ES cell line carrying Foxa2-Venus and Sox17-Cherry gene fusions
genotype/variation: Foxa2-Venus heterozygous;Sox17-Cherry homozygous
facs sorting markers: Foxa2-Venus-pos/Sox17-Cherry-neg
time point: d3
chip antibody: anti-H3K4me1 (Diagenode; Pab-037-050)
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| Growth protocol |
The cells were cultured for few consecutive passages on gelatine and ES medium. On the day of differentiation, mESCs were seeded on 10 cm gelatine coated dishes directly in endoderm differentiation medium (EDM) supplemented with 1 ng/ml of murine Wnt3a and 10 ng/ml of Activin A. Freshly prepared EDM supplemented with Wnt3a and Activin A was added every day. Cells were collected on day0, day3 and day5 for FACS isolation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1-2 million FACS-sorted cross-linked cells (1% formaldehyde, 10min RT) were lysed in 100 ul Buffer-B (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1%SDS, 1x protease inhibitors -Roche) and sonicated in a microtube (Covaris; 520045) using a Covaris S220 device until most of the DNA fragments were 200-500 base pairs long (settings: temperature 4°C, duty cycle 2%, peak incident power 105 Watts, cycles per burst 200). After shearing, lysates were centrifuged 10min, 4°C, 12000g and supernatant diluted with 900ul of Buffer-A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors-Roche). 150 ul of sonicated chromatin was then incubated 4h at 4°C on a rotating wheel with 3 µg of antibody conjugated to 10 µl of magnetic beads (Dynabeads, Life Technology). Beads were washed four times with Buffer-A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors-Roche) and once with Buffer-C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were re-suspended in 100µl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) and incubated 20min at 65 °C. Supernatant was transferred to a new tube. Crosslink reversal of immunoprecipitated DNA was carried out overnight at 65°C. Then 100µl TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA) was added, RNA was degraded by 4μl RNase A (10mg/ml) for 1 hour at 37°C and proteins were digested with 4μl Proteinase K (10 mg/ml) at 55°C for 2 hours. Finally, DNA was isolated by phenol:chloroform:Isoamyl alcohol purification followed by ethanol precipitation. Purified DNA was used as input for library preparation.
MicroPlex Library Preparation Kit v2 (Diagenode, cat. C05010012).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl.
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| Submission date |
Jun 25, 2018 |
| Last update date |
Aug 12, 2019 |
| Contact name |
Filippo M. Cernilogar |
| E-mail(s) |
[email protected]
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| Organization name |
LMU Munich
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| Department |
Biomedical Center
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| Street address |
Grosshaderner Strasse 9
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| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE116257 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ChIP-seq Histone-Modifications] |
| GSE116262 |
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 |
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| Relations |
| BioSample |
SAMN09486891 |
| SRA |
SRX4298450 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3223307_H3K4me1.d3F.r1.ucsc.bigWig |
640.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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